Make the .tag file
for your own project:
Here is a sample
Tag file
and raw data for
Estrogen Receptor (ER) ChIP-chip on Affymetrix Chromosomes 21 and 22 arrays.
Please make your own tag file (plain-text with a .tag suffix) according to this example using
any plain-text editor.

Running MAT by
typing 'MAT tag_files'. You can even specify multiple tag
files to MAT. You should be able to run MAT on the above ER
raw data.